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project:bioosm:start [2023/04/24 16:46] – geojson support + fixes sachyproject:bioosm:start [2023/05/28 14:58] – make it compatible with Centos 7 sachy
Line 188: Line 188:
  
 function getgeo () { function getgeo () {
- g=$(echo "$1 $2" | gdallocationinfo -wgs84 ./geo/eusr5000_600dpi_cesko_8b_geo.tif | grep -v 255 | grep -oPe '[0-9]+$')+ #g=$(echo "$1 $2" | gdallocationinfo -wgs84 ./geo/eusr5000_600dpi_cesko_8b_geo.tif | grep -v 255 | grep -oPe '[0-9]+$') 
 + g=$(echo "$1 $2" | gdallocationinfo -wgs84 ./geo/eusr5000_600dpi_cesko_8b_geo.tif | grep -v 255 | grep -oE '[0-9]+$')
  case "$g" in  case "$g" in
  "1")  "1")
Line 245: Line 246:
  fi  fi
  
- entryid=$(echo "$radek" | grep -oPe '<entry id="[0-9]+">' | grep -oPe '[0-9]+') + entryid=$(echo "$radek" | sed -E 's/^.*<entry id="([0-9]+)">.*$/\1/g;t;d') 
- co=$(echo "$radek" | grep -oe ' <title>.*</title> ' | sed -E 's/( )*<(\/)?title>( )*//g')+ co=$(echo "$radek" | sed -E 's/^.*<title>(.*)<\/title>.*$/\1/g;t;d')
  co=$(safehtml "$co")  co=$(safehtml "$co")
- obr=$(echo "$radek" | grep -oe ' <image>.*</image> ' | sed -E 's/( )*<(\/)?image>( )*//g' | grep -oPe '[^/]*$') + obr=$(echo "$radek" | sed -E 's/^.*<image>(.*)<\/image>.*$/\1/g;t;d' | sed -E 's/^.*\///g') 
- kde=$(echo "$radek" | grep -oe '<locality>.*</locality>' | grep -oPe '[0-9]+\.[0-9]+[, ]*[0-9]+\.[0-9]+')+ kde=$(echo "$radek" | sed -E 's/^.*<locality>(.*)<\/locality>.*$/\1/g;t;d')
  kde=$(safehtml "$kde")  kde=$(safehtml "$kde")
- kdex=$(echo "$kde" | grep -oPe '[0-9]+\.[0-9]+$') + kdex=$(echo "$kde" | sed -E 's/^[0-9]+\.[0-9]+[, ]*//g;t;d') # keep second part 
- kdex=$(safehtml "$kdex") + kdey=$(echo "$kde" | sed -E 's/[, ]*[0-9]+\.[0-9]+$//g;t;d') # keep first part 
- kdey=$(echo "$kde" | grep -oPe '^[0-9]+\.[0-9]+') + kdy=$(echo "$radek" | sed -E 's/^.*<taken-date>(.*)<\/taken-date>.*$/\1/g;t;d' | sed -E 's/([0-9]+)\.([0-9]+)\.([0-9]{4})/\3-\2-\1/g' | sed -E 's/-([0-9])-/-0\1-/g' | sed -E 's/-([0-9])$/-0\1/g')
- kdey=$(safehtml "$kdey") +
- kdy=$(echo "$radek" | grep -oe ' <taken-date>.*</taken-date> ' | sed -E 's/( )*<(\/)?taken-date>( )*//g' | sed -E 's/([0-9]+)\.([0-9]+)\.([0-9]{4})/\3-\2-\1/g' | sed -E 's/-([0-9])-/-0\1-/g' | sed -E 's/-([0-9])$/-0\1/g')+
  kdy=$(safehtml "$kdy")  kdy=$(safehtml "$kdy")
- skop_typ=$(echo "$radek" | grep -oe ' <new-field-1>.*</new-field-1> ' | sed -E 's/( )*<(\/)?new-field-1>( )*//g')+ skop_typ=$(echo "$radek" | sed -E 's/^.*<new-field-1>(.*)<\/new-field-1>.*$/\1/g;t;d')
  skop_typ=$(safehtml "$skop_typ")  skop_typ=$(safehtml "$skop_typ")
- skop=$(echo "$radek" | grep -oe ' <microscope>.*</microscope> ' | sed -E 's/( )*<(\/)?microscope>( )*//g')+ skop=$(echo "$radek" | sed -E 's/^.*<microscope>(.*)<\/microscope>.*$/\1/g;t;d')
  skop=$(safehtml "$skop")  skop=$(safehtml "$skop")
- imp=$(echo "$radek" | grep -oe ' <new-field-3>.*</new-field-3> ' | sed -E 's/( )*<(\/)?new-field-3>( )*//g')+ imp=$(echo "$radek" | sed -E 's/^.*<new-field-3>(.*)<\/new-field-3>.*$/\1/g;t;d')
  imp=$(safehtml "$imp")  imp=$(safehtml "$imp")
- reg=$(echo "$radek" | grep -oe ' <new-field-4>.*</new-field-4> ' | sed -E 's/( )*<(\/)?new-field-4>( )*//g')+ reg=$(echo "$radek" | sed -E 's/^.*<new-field-4>(.*)<\/new-field-4>.*$/\1/g;t;d')
  reg=$(safehtml "$reg")  reg=$(safehtml "$reg")
- phy=$(echo "$radek" | grep -oe ' <phylum>.*</phylum> ' | sed -E 's/( )*<(\/)?phylum>( )*//g')+ phy=$(echo "$radek" | sed -E 's/^.*<phylum>(.*)<\/phylum>.*$/\1/g;t;d')
  phy=$(safehtml "$phy")  phy=$(safehtml "$phy")
- cla=$(echo "$radek" | grep -oe ' <class>.*</class> ' | sed -E 's/( )*<(\/)?class>( )*//g')+ cla=$(echo "$radek" | sed -E 's/^.*<class>(.*)<\/class>.*$/\1/g;t;d')
  cla=$(safehtml "$cla")  cla=$(safehtml "$cla")
- ord=$(echo "$radek" | grep -oe ' <order>.*</order> ' | sed -E 's/( )*<(\/)?order>( )*//g')+ ord=$(echo "$radek" | sed -E 's/^.*<order>(.*)<\/order>.*$/\1/g;t;d')
  ord=$(safehtml "$ord")  ord=$(safehtml "$ord")
- fam=$(echo "$radek" | grep -oe ' <family>.*</family> ' | sed -E 's/( )*<(\/)?family>( )*//g')+ fam=$(echo "$radek" | sed -E 's/^.*<family>(.*)<\/family>.*$/\1/g;t;d')
  fam=$(safehtml "$fam")  fam=$(safehtml "$fam")
- gen=$(echo "$radek" | grep -oe ' <genus>.*</genus> ' | sed -E 's/( )*<(\/)?genus( )*>//g')+ gen=$(echo "$radek" | sed -E 's/^.*<genus>(.*)<\/genus>.*$/\1/g;t;d')
  gen=$(safehtml "$gen")  gen=$(safehtml "$gen")
- spe=$(echo "$radek" | grep -oe ' <species>.*</species> ' | sed -E 's/( )*<(\/)?species>( )*//g')+ spe=$(echo "$radek" | sed -E 's/^.*<species>(.*)<\/species>.*$/\1/g;t;d')
  spe=$(safehtml "$spe")  spe=$(safehtml "$spe")
- loc=$(echo "$radek" | grep -oe ' <locality---plaintext>.*</locality---plaintext> ' | sed -E 's/( )*<(\/)?locality---plaintext>( )*//g')+ loc=$(echo "$radek" | sed -E 's/^.*<locality---plaintext>(.*)<\/locality---plaintext>.*$/\1/g;t;d')
  loc=$(safehtml "$loc")  loc=$(safehtml "$loc")
- des=$(echo "$radek" | grep -oe ' <description>.*</description> ' | sed -E 's/( )*<(\/)?description>( )*//g')+ des=$(echo "$radek" | sed -E 's/^.*<description>(.*)<\/description>.*$/\1/g;t;d')
  des=$(safehtml "$des")  des=$(safehtml "$des")
- vid=$(echo "$radek" | grep -oe ' <videolink>.*</videolink> ' | sed -E 's/( )*<(\/)?videolink>( )*//g')+ vid=$(echo "$radek" | sed -E 's/^.*<videolink>(.*)<\/videolink>.*$/\1/g;t;d')
  vid=$(safehtml "$vid")  vid=$(safehtml "$vid")
- bio=$(echo "$radek" | grep -oe ' <biotope>.*</biotope> ' | sed -E 's/( )*<(\/)?biotope>( )*//g')+ bio=$(echo "$radek" | sed -E 's/^.*<biotope>(.*)<\/biotope>.*$/\1/g;t;d')
  bio=$(safehtml "$bio")  bio=$(safehtml "$bio")
- eng=$(echo "$radek" | grep -oe ' <enlargement>.*</enlargement> ' | sed -E 's/( )*<(\/)?enlargement>( )*//g')+ eng=$(echo "$radek" | sed -E 's/^.*<enlargement>(.*)<\/enlargement>.*$/\1/g;t;d')
  eng=$(safehtml "$eng")  eng=$(safehtml "$eng")
- obs=$(echo "$radek" | grep -oe ' <observer>.*</observer> ' | sed -E 's/( )*<(\/)?observer>( )*//g')+ obs=$(echo "$radek" | sed -E 's/^.*<observer>(.*)<\/observer>.*$/\1/g;t;d')
  obs=$(safehtml "$obs")  obs=$(safehtml "$obs")
- lnk=$(echo "$radek" | grep -oe ' <localitylink>.*</localitylink> ' | sed -E 's/( )*<(\/)?localitylink>( )*//g')+ lnk=$(echo "$radek" | sed -E 's/^.*<localitylink>(.*)<\/localitylink>.*$/\1/g;t;d')
  lnk=$(safehtml "$lnk")  lnk=$(safehtml "$lnk")
- har=$(echo "$radek" | grep -oe ' <harvesting-method>.*</harvesting-method> ' | sed -E 's/( )*<(\/)?harvesting-method>( )*//g') + har=$(echo "$radek" | sed -E 's/^.*<harvesting-method>(.*)<\/harvesting-method>.*$/\1/g;t;d') 
- den=$(echo "$radek" | grep -oe ' <population-density>.*</population-density> ' | sed -E 's/( )*<(\/)?population-density>( )*//g') + den=$(echo "$radek" | sed -E 's/^.*<population-density>(.*)<\/population-density>.*$/\1/g;t;d') 
- dur=$(echo "$radek" | grep -oe ' <min>.*</min> ' | sed -E 's/( )*<(\/)?min>( )*//g') + dur=$(echo "$radek" | sed -E 's/^.*<min>(.*)<\/min>.*$/\1/g;t;d') 
- lor=$(echo "$radek" | grep -oe ' <locality-reference>.*</locality-reference> ' | sed -E 's/( )*<(\/)?locality-reference>( )*//g') + lor=$(echo "$radek" | sed -E 's/^.*<locality-reference>(.*)<\/locality-reference>.*$/\1/g;t;d') 
- lrl=$(echo "$radek" | grep -oe ' <locality-reference---link>.*</locality-reference---link> ' | sed -E 's/( )*<(\/)?locality-reference---link>( )*//g') + lrl=$(echo "$radek" | sed -E 's/^.*<locality-reference---link>(.*)<\/locality-reference---link>.*$/\1/g;t;d') 
- lov=$(echo "$radek" | grep -oe ' <locality---vobrazek>.*</locality---vobrazek> ' | sed -E 's/( )*<(\/)?locality---vobrazek>( )*//g' | grep -oPe '[^/]*$')+ lov=$(echo "$radek" | sed -E 's/^.*<locality---vobrazek>(.*)<\/locality---vobrazek>.*$/\1/g;t;d' | sed -E 's/^.*\///g')
  lov=$(safehtml "$lov")  lov=$(safehtml "$lov")
- cls=$(echo "$radek" | grep -oe ' <cluster>.*</cluster> ' | grep -oPe '[0-9]*')+ cls=$(echo "$radek" | sed -E 's/^.*<cluster>([0-9]*)<\/cluster>.*$/\1/g;t;d')
  mpi=$(echo "$radek" | grep -oe ' <mainpic>yep</mainpic> ')  mpi=$(echo "$radek" | grep -oe ' <mainpic>yep</mainpic> ')
- elv=$(echo "$kdex $kdey" | gdallocationinfo -wgs84 ./elev/cesko_big.tiff | grep "Value" | grep -oPe '[0-9]+$')+ elv=$(echo "$kdex $kdey" | gdallocationinfo -wgs84 ./elev/cesko_big.tiff | grep "Value" | grep -oe '[0-9]+$')
  geo=$(getgeo "$kdex" "$kdey")  geo=$(getgeo "$kdex" "$kdey")
- gra=$(echo "$radek" | grep -oe ' <grant>.*</grant> ' | sed -E 's/( )*<(\/)?grant>( )*//g') + gra=$(echo "$radek" | sed -E 's/^.*<grant>(.*)<\/grant>.*$/\1/g;t;d') 
- tem=$(echo "$radek" | grep -oe ' <temperature>.*</temperature> ' | sed -E 's/( )*<(\/)?temperature>( )*//g') + tem=$(echo "$radek" | sed -E 's/^.*<temperature>(.*)<\/temperature>.*$/\1/g;t;d') 
- cnd=$(echo "$radek" | grep -oe ' <conductivity>.*</conductivity> ' | sed -E 's/( )*<(\/)?conductivity>( )*//g') + cnd=$(echo "$radek" | sed -E 's/^.*<conductivity>(.*)<\/conductivity>.*$/\1/g;t;d') 
- ph=$(echo "$radek" | grep -oe ' <ph>.*</ph> ' | sed -E 's/( )*<(\/)?ph>( )*//g') + ph=$(echo "$radek" | sed -E 's/^.*<ph>(.*)<\/ph>.*$/\1/g;t;d') 
- kar=$(echo "$radek" | grep -oe ' <karyotype>.*</karyotype> ' | sed -E 's/( )*<(\/)?karyotype>( )*//g') + kar=$(echo "$radek" | sed -E 's/^.*<karyotype>(.*)<\/karyotype>.*$/\1/g;t;d') 
- lid=$(echo "$radek" | grep -oe ' <localityid>.*</localityid> ' | sed -E 's/( )*<(\/)?localityid>( )*//g')+ lid=$(echo "$radek" | sed -E 's/^.*<localityid>(.*)<\/localityid>.*$/\1/g;t;d')
  
- # >&2 echo "$co - $har - $den - $dur - $lor - $lrl - $lov - $elv"+  #>&2 echo "$co - $har - $den - $dur - $lor - $lrl - $lov - $elv" 
 + #continue;
  
  detid=$(echo "brmlab$co$obr$kde$kdy" | md5sum | grep -oe '[a-zA-Z0-9]*')  detid=$(echo "brmlab$co$obr$kde$kdy" | md5sum | grep -oe '[a-zA-Z0-9]*')
Line 340: Line 340:
  if [[ "$phy" = "Platyhelminthes" ]]; then  if [[ "$phy" = "Platyhelminthes" ]]; then
  povr=$(cat "./povodi_r.json" | ./povodi.py "$kdey" "$kdex")  povr=$(cat "./povodi_r.json" | ./povodi.py "$kdey" "$kdex")
- povrf=$(echo "$povr" | grep -oPe '^[^ ]*' | tr 'e' 'E')+ #povrf=$(echo "$povr" | grep -oPe '^[^ ]*' | tr 'e' 'E') 
 + povrf=$(echo "$povr" | sed -e 's/ .*$//g' | tr 'e' 'E')
  povrn=$(echo "$povr" | sed -e 's/^[^ ]* //g')  povrn=$(echo "$povr" | sed -e 's/^[^ ]* //g')
  povs=$(cat "./povodi_s.json" | ./povodi.py "$kdey" "$kdex")  povs=$(cat "./povodi_s.json" | ./povodi.py "$kdey" "$kdex")
- povsf=$(echo "$povs" | grep -oPe '^[^ ]*' | tr 'e' 'E')+ #povsf=$(echo "$povs" | grep -oPe '^[^ ]*' | tr 'e' 'E') 
 + povsf=$(echo "$povs" | sed -e 's/ .*$//g' | tr 'e' 'E')
  povsn=$(echo "$povs" | sed -e 's/^[^ ]* //g')  povsn=$(echo "$povs" | sed -e 's/^[^ ]* //g')
  if (( $(echo "$povsf < $povrf" | bc -l) )) ; then  if (( $(echo "$povsf < $povrf" | bc -l) )) ; then
Line 594: Line 596:
  
 # Sorted unique Kingdoms (to be passed as selection criteria) # Sorted unique Kingdoms (to be passed as selection criteria)
-kingdoms=$(unzip -p "$1" tellico.xml | grep -oe '<new-field-4>.*</new-field-4>' | sed -E 's/( )*<(\/)?new-field-4>( )*//g' | sort | uniq)+#kingdoms=$(unzip -p "$1" tellico.xml | grep -oe '<new-field-4>.*</new-field-4>' | sed -E 's/( )*<(\/)?new-field-4>( )*//g' | sort | uniq) 
 +kingdoms=$(unzip -p "$1" tellico.xml | sed -E 's/^.*<new-field-4>(.*)<\/new-field-4>.*$/\1/g;t;d' | sort | uniq)
  
 echo '<!DOCTYPE html>' echo '<!DOCTYPE html>'
Line 661: Line 664:
 granty=$(unzip -p "$1" tellico.xml | grep "<grant>" | sed -E 's/( )*<(\/)?grant>( )*//g' | sed -E 's/_additional$//g' | sort -u | grep -v "^none$") granty=$(unzip -p "$1" tellico.xml | grep "<grant>" | sed -E 's/( )*<(\/)?grant>( )*//g' | sed -E 's/_additional$//g' | sort -u | grep -v "^none$")
 #praseTC=$(unzip -p "$1" tellico.xml | tr -d '\n' | sed -e $'s/<entry id="/\\\n<entry id="/g' -e $'s/<\/entry>/<\/entry>\\\n/g' | grep -Pe '^<entry id="' | grep "<strcit-do-mapy>yep</strcit-do-mapy>" | sed -E 's/(^.*)(<locality>.*<\/locality>)(.*$)/\2\1\3/' | sort) #praseTC=$(unzip -p "$1" tellico.xml | tr -d '\n' | sed -e $'s/<entry id="/\\\n<entry id="/g' -e $'s/<\/entry>/<\/entry>\\\n/g' | grep -Pe '^<entry id="' | grep "<strcit-do-mapy>yep</strcit-do-mapy>" | sed -E 's/(^.*)(<locality>.*<\/locality>)(.*$)/\2\1\3/' | sort)
-praseTC=$(unzip -p "$1" tellico.xml | tr -d '\n' | sed -e $'s/<entry id="/\\\n<entry id="/g' -e $'s/<\/entry>/<\/entry>\\\n/g' | grep -Pe '^<entry id="' | sed -E 's/(^.*)(<locality>.*<\/locality>)(.*$)/\2\1\3/' | sort)+#praseTC=$(unzip -p "$1" tellico.xml | tr -d '\n' | sed -e $'s/<entry id="/\\\n<entry id="/g' -e $'s/<\/entry>/<\/entry>\\\n/g' | grep -Pe '^<entry id="' | sed -E 's/(^.*)(<locality>.*<\/locality>)(.*$)/\2\1\3/' | sort) 
 +praseTC=$(unzip -p "$1" tellico.xml | tr -d '\n' | sed -e $'s/<entry id="/\\\n<entry id="/g' -e $'s/<\/entry>/<\/entry>\\\n/g' | grep -E '^<entry id="' | sed -E 's/(^.*)(<locality>.*<\/locality>)(.*$)/\2\1\3/' | sort)
  
  
Line 673: Line 677:
 while IFS='' read -r grnt || [[ -n "$grnt" ]]; do while IFS='' read -r grnt || [[ -n "$grnt" ]]; do
  # 'nope' pokud to ma byt jen na grantstrance ale ne ve velkem bioosm  # 'nope' pokud to ma byt jen na grantstrance ale ne ve velkem bioosm
- vepr=$(echo "$praseTC" | grep -Pe "<strcit-do-mapy>(yep)|(negative)|(nope)</strcit-do-mapy>" | grep -Pe "<grant>$grnt(_additional)?</grant>")+ #vepr=$(echo "$praseTC" | grep -Pe "<strcit-do-mapy>(yep)|(negative)|(nope)</strcit-do-mapy>" | grep -Pe "<grant>$grnt(_additional)?</grant>") 
 + vepr=$(echo "$praseTC" | grep -E "<strcit-do-mapy>(yep)|(negative)|(nope)</strcit-do-mapy>" | grep -E "<grant>$grnt(_additional)?</grant>")
  spagety "$vepr" "$grnt" "$ICON_biohazard"  spagety "$vepr" "$grnt" "$ICON_biohazard"
 done <<< $(echo "$granty") done <<< $(echo "$granty")
project/bioosm/start.txt · Last modified: 2023/09/21 12:15 by sachy